Table 2.
Network-based methods for patient stratification and biomarker identification (prognostic, therapeutic, progression).
| Method | Application | Approach | URL | Reference |
|---|---|---|---|---|
| NBS | Patient stratification | Clustering patients based on network-smoothed mutation profiles | http://chianti.ucsd.edu/~mhofree/NBS/ | [97] |
| NetNorM | Patient stratification | NBS with mutation profile normalization instead of network smoothing | https://github.com/marineLM/NetNorM | [98] |
| He et al. | Patient stratification | NBS using cancer-type-specific co-expression networks | - | [100] |
| NCIS | Patient stratification | Network-informed co-clustering using expression data | http://bioen-compbio.bioen.illinois.edu/NCIS/* | [102] |
| NetBC | Patient stratification | Network-informed bi-clustering using expression data | http://mlda.swu.edu.cn/codes.php?name=NetBC* | [103] |
| PARADIGM | Patient stratification | Data integration; mutation and pathway-level activities | http://sbenz.github.io/Paradigm/ | [104] |
| SNF | Patient stratification | Data integration; multi-omic patient similarity networks | http://compbio.cs.toronto.edu/SNF/SNF/Software.html | [105] |
| ndmaSNF | Patient stratification | SNF framework with addition of somatic mutation data | - | [106] |
| Zhong et al. | Patient stratification | NBS using small panels of exome-level data | - | [99] |
| DrugComboRanker | Therapeutic biomarkers | Integrating disease signaling network data and transcriptomic expression data | Available upon request. | [109] |
| EPN | Therapeutic biomarkers | Integrating disease signaling network data and transcriptomic expression data | Available upon request. | [110] |
| Wu et al. | Therapeutic biomarkers | Data integration; protein interactions, protein-DNA interactions, and signaling pathways | - | [111] |
| Choi et al. | Therapeutic biomarkers | Network perturbation analysis | Available upon request. | [112] |
| Chen et al. | Therapeutic biomarkers | Pathway-pathway interaction network-based synergy evaluation | - | [113] |
| SimpleBool | Therapeutic biomarkers | Boolean network analysis on a knowledge-based network | https://github.com/SimpleBool/SimpleBool | [114] |
| Choi et al. | Therapeutic biomarkers | Boolean network modeling and attractor landscape analysis | Available upon request. | [115] |
| IMAHP | Therapeutic biomarkers | Protein co-regulation analysis to explore drug sensitivities | - | [116] |
| Lee et al. | Therapeutic biomarkers | Effect of time-staggered application of drugs on therapeutic response | - | [119] |
| Roumeliotis et al. | Variant Interpretation | Impact of genomic alterations on protein networks | - | [117] |
| Engin et al. | Variant Interpretation | Diffusion to evaluate downstream consequences of network perturbations | - | [118] |
| mCGfinder | Subtype biomarkers | Matrix decomposition to prioritize alterations concentrated in subsets of patients | https://github.com/USTC-HIlab/mCGfinder | [123] |
| Sun et al. | Subtype biomarkers | Weighted gene co-expression network analysis (WGCNA) | https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/ | [124] |
| CAERUS | Subtype biomarkers | Co-expression analysis of marker genes and network neighbors | http://www.oicr.on.ca/research/ouellette/caerus* | [125] |
| Net-Cox | Survival analysis | Network-informed Cox regression | http://compbio.cs.umn.edu/Net-Cox/ | [127] |
| DegreeCox | Survival analysis | Network-informed Cox regression | http://sels.tecnico.ulisboa.pt/gitlab/averissimo/degree-cox | [128] |
| Gade et al. | Survival analysis | Data integration; mRNA and miRNA expression profiles | https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-12-488/MediaObjects/12859_2011_5167_MOESM1_ESM.R | [121] |
| GIREN | Survival analysis | Data integration; gene measurements and interaction information | https://github.com/lzcyzm/GIREN | [129] |
| Huang et al. | Survival analysis | Pathway-based Cox regression | - | [130] |
| Eng et al. | Survival analysis | Pathway-based Cox regression | - | [131] |
| Zhang et al. | Survival analysis | Pathway-based Cox regression | http://www.ssg.uab.edu/bhglm/ | [132] |
| Yang et al. | Prognostic biomarkers | Time series analysis for dynamic network biomarkers indicating imminent state change | - | [133] |
| Chuang et al. | Prognositic biomarkers | Detection of subnetworks associated with metastatic breast cancer | - | [122] |
| Wu et al. | Prognostic biomarkers | Proximity to known cancer genes in interaction network | - | [46] |
| Yuan et al. | Prognostic biomarkers | Filtering a global interaction network against curated annotations | - | [135] |
| Zhou et al. | Prognostic biomarkers | Data integration; mRNA, miRNA and long non-coding RNA interactions | - | [136] |
*
Link listed in the original publication of the method is not valid.